Reference

Prerequisites

High level overview of the package

rcompendium-package

Create a package or research compendium structure

Setup functions

These four functions are usually the only ones user needs to run. The use of set_credentials is strongly recommended to permanently store user information (name, email, orcid, etc.) in the .Rprofile. This function must be run one time. The function new_package must be used to create an R package structure whereas new_compendium creates a new research compendium structure (i.e. R package structure with some additional files/folders). After that user can start to develop his/her project and run refresh to frequently update the package/compendium components (Rd files, NAMESPACE, dependencies, badges, README.md, etc.)

set_credentials()

Store credentials to the .Rprofile

new_package()

Create an R package structure

new_compendium()

Create an R compendium structure

refresh()

Refresh a package/research compendium

Create files

These function write files specific to R package and research compendium (add_makefile). They are called by the main functions new_package, new_compendium, and refresh but they also can be used to overwrite files (with overwrite = TRUE) in case of broken code. When open = TRUE and overwrite = FALSE (default) files are open in the editor.

add_description()

Create a DESCRIPTION file

add_license()

Add a LICENSE

add_package_doc()

Create a package-level documentation file

add_citation()

Create a CITATION file

add_testthat()

Initialize units tests

add_vignette()

Create a vignette document

add_readme_rmd()

Create a README file

add_compendium()

Create compendium folders

add_makefile()

Create a Make-like R file

add_renv()

Initialize renv

add_dockerfile()

Create a Dockerfile

README badges

These functions add badges to the README.Rmd. They are called by the main functions new_package, new_compendium, and refresh but they also can be used to update badges if license, lifecycle, repository status change or to update number of dependencies (add_dependencies_badge).

add_cran_badge()

Add a CRAN Status badge

add_dependencies_badge()

Add a Dependencies badge

add_license_badge()

Add a License badge

add_lifecycle_badge()

Add a Life Cycle badge

add_repostatus_badge()

Add a Repository Status badge

add_github_actions_check_badge()

Add a R CMD Check badge

add_github_actions_pkgdown_badge()

Add a Website badge

add_github_actions_codecov_badge()

Add a Test coverage badge

add_codecov_badge()

Add a Codecov badge

Advanced functions

These functions update fields in DESCRIPTION (add_dependencies and add_r_depend), edit files (add_to_gitignore and add_to_buildignore), or write configuration files (add_github_actions_check, add_github_actions_pkgdown, add_github_actions_codecov, and add_github_actions_render).

add_dependencies()

Add dependencies in DESCRIPTION

add_r_depend()

Add minimal R version to DESCRIPTION

add_to_gitignore()

Add to the .gitignore file

add_to_buildignore()

Add to the .Rbuildignore file

add_github_actions_check()

Setup GitHub Actions to check package

add_github_actions_pkgdown()

Setup GitHub Actions to build and deploy package website

add_github_actions_codecov()

Setup GitHub Actions to report code coverage

add_github_actions_render()

Setup GitHub Actions to render README

Utilities functions

These functions return objects but do not edit any file.

get_licenses()

List all available licenses

get_all_dependencies()

Get all external dependencies

get_all_functions()

List all functions in the package

get_minimal_r_version()

Get required minimal R version